fit_models {AICcPermanova}

Fit PERMANOVA models and arrange by AICc

Description

This function fits PERMANOVA models for all combinations of variables in a given dataset, and arranges the models by Akaike Information Criterion (AICc) score. The function also calculates the maximum variance inflation factor (max_vif) for each model.

Usage

fit_models(
  all_forms,
  veg_data,
  env_data,
  method = "bray",
  ncores = 2,
  log = TRUE,
  logfile = "log.txt",
  multiple = 100,
  strata = NULL,
  verbose = FALSE
)

Arguments

all_forms

A data frame generated by make_models

veg_data

A dataset with vegetation presence absense or abundance data

env_data

A dataset with the variables described in all_froms

method

method for distance from vegdist

ncores

An integer specifying the number of cores to use for parallel processing

log

logical if true, a log file will be generated

logfile

the text file that will be generated as a log

multiple

after how many loops to write a log file

strata

a block variable similar to the use in adonis2

verbose

logical, defaults TRUE, sends messages about processing times

Value

A data.frame with fitted models arranged by AICc, including the formula used, the number of explanatory variables, R2, adjusted R2, and the AICc and max VIF.

References

Anderson, M. J. (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecology, 26(1), 32-46. https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x

Examples

library(vegan)
data(dune)
data(dune.env)

AllModels <- make_models(vars = c("A1", "Moisture", "Manure"))

fit_models(all_forms = AllModels,
           veg_data = dune,
           env_data = dune.env)